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<h1>mmp file format</h1>
<p>
An mmp file consists of a sequence of parts. Each is typically a
connected molecule. The simulator will check for van der Waals
interactions between atoms of different parts, but not within a given
part. If such interactions are expected, the "waals" record can be
used.
</p>
<p>
Each part is a "part" record followed by atom and bond records. The
bonds must be back-references, i.e. if atom 1 and atom 2 are bonded,
atom 1 will have no bond record, and atom 2 will have a record
pointing back to atom 1.
</p>
<p>
The intent in calling the bond records "bond1" was that there are
intended to be bond2, bond3, and bond4 for double, triple, and
aromatic bonds.
</p>
<h2>record types</h2>
Note parentheses and commas are required. Braces are metacomments.
<ul>
<li><font size="+1"><strong>part </strong> <em> xxx comment</em></font>
<ul> <li>
xxx is "vdw", "bns", or "nil" (see show)
</li></ul>
</li>
<li>
<font size="+1"><strong>atom </strong> <em> n (e) (x, y, z)</em></font>
<ul> <li>
n is atom number -- intended to rise sequentially from 1
</li><li>
e is element number, e.g. carbon = 6
</li><li>
x, y, z, the position in 1e-13m
</li></ul>
</li>
<li><font size="+1"><strong>bond1 </strong> <em> atom# atom# ... {up
to 25}</em></font>
<ul><li>
bonds the last-defined atom to the indicated ones
</li></ul>
</li>
<li><font size="+1"><strong>waals </strong> <em> atom# atom# ... {up to 25}</em></font>
<ul><li>
indicates vanderwaals interaction to be simulated between
indicated and last-defined atoms
(NB vdW interactions are automatically simulated between atoms
of different parts)
</li></ul>
</li>
<li><font size="+1"><strong>show </strong> <em> xxx</em></font>
<ul><li>
xxx is "vdw" (van der Waals), "bns" (ball and stick), or "nil"
(don't show). Applies to all atoms until the next show or part record.
</li></ul>
</li>
<li><font size="+1"><strong>ground </strong> <em> atom# atom# ... {up to 25}</em></font>
<ul><li>
given atoms are "welded to space"
</li></ul>
</li>
<li><font size="+1"><strong>motor </strong> <em> torque, speed, (cx,
cy, cz) (ax, ay, az) </em></font>
<ul><li>
torque in nN*nm (float)
</li><li>
speed in gHz (float)
</li><li>
cx, cy, cz is center of rotation (same format as atom posns)
</li><li>
ax, xy, az is axis of rotation (ditto)
</li></ul>
</li>
<li><font size="+1"><strong>shaft </strong> <em> atom# atom# ... </em></font>
<p>(up to 25) (must follow motor immediately)</p>
<ul><li>
atoms to which the motor is connected
</li></ul>
</li>
<li><font size="+1"><strong>kelvin </strong> <em> n</em></font>
<ul><li>
n is temperature in kelvins (int)
</li></ul>
</li>
<li><font size="+1"><strong>end </strong></font>
<ul><li>
logical end of file
</li></ul>
</li></ul>
<h2>unimplemented:</h2>
<ul>
<li><font size="+1"><strong>link </strong> <em> (x1, y1, z1) (x2, y2, z2)</em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li>
<li><font size="+1"><strong>bearing </strong> <em> (cx, cy, cz) (ax, ay, az) </em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li>
<li><font size="+1"><strong>ball </strong> <em> (cx, cy, cz)</em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li>
<li><font size="+1"><strong>linear </strong> <em> (ax, ay, az)</em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li>
<li><font size="+1"><strong>planar </strong> <em> (nx, ny, nz) </em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li>
<li><font size="+1"><strong>hooke </strong> <em>(cx, cy, cz) (a1x, a1y, a1z) (a2x, a2y, a2z) </em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li>
<li><font size="+1"><strong>prism </strong> <em>(ax, ay, az)</em></font>
<ul><li>
shaft ...
</li><li>
shaft ... or ground
</li></ul>
</li></ul>
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